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JAL-2388 Make startRes,startSeq,endRes,endSeq private with get/setters
author
kiramt
<k.mourao@dundee.ac.uk>
Mon, 27 Feb 2017 16:10:21 +0000
(16:10 +0000)
committer
kiramt
<k.mourao@dundee.ac.uk>
Mon, 27 Feb 2017 16:10:21 +0000
(16:10 +0000)
17 files changed:
src/jalview/appletgui/AlignFrame.java
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src/jalview/appletgui/AlignViewport.java
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src/jalview/appletgui/AlignmentPanel.java
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src/jalview/appletgui/AnnotationPanel.java
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src/jalview/appletgui/IdCanvas.java
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src/jalview/appletgui/OverviewPanel.java
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src/jalview/appletgui/SeqCanvas.java
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src/jalview/appletgui/SeqPanel.java
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src/jalview/gui/AlignFrame.java
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src/jalview/gui/AlignViewport.java
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src/jalview/gui/AlignmentPanel.java
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src/jalview/gui/AnnotationPanel.java
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src/jalview/gui/IdCanvas.java
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src/jalview/gui/Jalview2XML.java
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src/jalview/gui/SeqCanvas.java
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src/jalview/gui/SeqPanel.java
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src/jalview/viewmodel/AlignmentViewport.java
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diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
6a0b390
..
dc622f5
100644
(file)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-571,8
+571,8
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.getStartRes();
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.getStartSeq();
}
break;
}
break;
@@
-598,8
+598,8
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
else
{
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ alignPanel.setScrollValues(viewport.getStartRes(),
+ 2 * viewport.getStartSeq() - viewport.getEndSeq());
}
break;
}
break;
@@
-610,8
+610,8
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
else
{
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
+ alignPanel.setScrollValues(viewport.getStartRes(),
+ viewport.getEndSeq());
}
break;
}
break;
@@
-2388,7
+2388,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(viewport.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
@@
-2420,7
+2420,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(viewport.getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
diff --git
a/src/jalview/appletgui/AlignViewport.java
b/src/jalview/appletgui/AlignViewport.java
index
951a651
..
f927e63
100644
(file)
--- a/
src/jalview/appletgui/AlignViewport.java
+++ b/
src/jalview/appletgui/AlignViewport.java
@@
-76,10
+76,10
@@
public class AlignViewport extends AlignmentViewport implements
alignment = al;
// we always pad gaps
this.setPadGaps(true);
alignment = al;
// we always pad gaps
this.setPadGaps(true);
- this.startRes = 0;
- this.endRes = al.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = al.getHeight() - 1;
+ this.setStartRes(0);
+ this.setEndRes(al.getWidth() - 1);
+ this.setStartSeq(0);
+ this.setEndSeq(al.getHeight() - 1);
if (applet != null)
{
// get the width and height scaling factors if they were specified
if (applet != null)
{
// get the width and height scaling factors if they were specified
diff --git
a/src/jalview/appletgui/AlignmentPanel.java
b/src/jalview/appletgui/AlignmentPanel.java
index
e97c347
..
af7e9cd
100644
(file)
--- a/
src/jalview/appletgui/AlignmentPanel.java
+++ b/
src/jalview/appletgui/AlignmentPanel.java
@@
-519,7
+519,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
vscroll.setValue(res / cwidth);
if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
vscroll.setValue(res / cwidth);
- av.startRes = vscroll.getValue() * cwidth;
+ av.setStartRes(vscroll.getValue() * cwidth);
}
}
}
}
@@
-632,8
+632,8
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
public void setWrapAlignment(boolean wrap)
{
public void setWrapAlignment(boolean wrap)
{
- av.startSeq = 0;
- av.startRes = 0;
+ av.setStartSeq(0);
+ av.setStartRes(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
@@
-832,8
+832,8
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
overviewPanel.setBoxPosition();
}
overviewPanel.setBoxPosition();
}
- int scrollX = av.startRes - oldX;
- int scrollY = av.startSeq - oldY;
+ int scrollX = av.getStartRes() - oldX;
+ int scrollY = av.getStartSeq() - oldY;
if (av.getWrapAlignment() || !fastPaint || av.MAC)
{
if (av.getWrapAlignment() || !fastPaint || av.MAC)
{
@@
-843,13
+843,13
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
// Make sure we're not trying to draw a panel
// larger than the visible window
{
// Make sure we're not trying to draw a panel
// larger than the visible window
- if (scrollX > av.endRes - av.startRes)
+ if (scrollX > av.getEndRes() - av.getStartRes())
{
{
- scrollX = av.endRes - av.startRes;
+ scrollX = av.getEndRes() - av.getStartRes();
}
}
- else if (scrollX < av.startRes - av.endRes)
+ else if (scrollX < av.getStartRes() - av.getEndRes())
{
{
- scrollX = av.startRes - av.endRes;
+ scrollX = av.getStartRes() - av.getEndRes();
}
idPanel.idCanvas.fastPaint(scrollY);
}
idPanel.idCanvas.fastPaint(scrollY);
@@
-955,8
+955,8
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
private void sendViewPosition()
{
StructureSelectionManager.getStructureSelectionManager(av.applet)
private void sendViewPosition()
{
StructureSelectionManager.getStructureSelectionManager(av.applet)
- .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
- av.endSeq);
+ .sendViewPosition(this, av.getStartRes(), av.getEndRes(),
+ av.getStartSeq(), av.getEndSeq());
}
/**
}
/**
diff --git
a/src/jalview/appletgui/AnnotationPanel.java
b/src/jalview/appletgui/AnnotationPanel.java
index
6012c1a
..
8b1bb26
100755
(executable)
--- a/
src/jalview/appletgui/AnnotationPanel.java
+++ b/
src/jalview/appletgui/AnnotationPanel.java
@@
-618,7
+618,7
@@
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
gg.setColor(Color.white);
gg.fillRect(0, 0, getSize().width, getSize().height);
gg.setColor(Color.white);
gg.fillRect(0, 0, getSize().width, getSize().height);
- drawComponent(gg, av.startRes, av.endRes + 1);
+ drawComponent(gg, av.getStartRes(), av.getEndRes() + 1);
g.drawImage(image, 0, 0, this);
}
g.drawImage(image, 0, 0, this);
}
@@
-635,7
+635,7
@@
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
gg.copyArea(0, 0, imgWidth, getSize().height,
-horizontal * av.getCharWidth(), 0);
gg.copyArea(0, 0, imgWidth, getSize().height,
-horizontal * av.getCharWidth(), 0);
- int sr = av.startRes, er = av.endRes + 1, transX = 0;
+ int sr = av.getStartRes(), er = av.getEndRes() + 1, transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
if (horizontal > 0) // scrollbar pulled right, image to the left
{
diff --git
a/src/jalview/appletgui/IdCanvas.java
b/src/jalview/appletgui/IdCanvas.java
index
d72e91f
..
8f8ed35
100755
(executable)
--- a/
src/jalview/appletgui/IdCanvas.java
+++ b/
src/jalview/appletgui/IdCanvas.java
@@
-106,13
+106,14
@@
public class IdCanvas extends Panel
gg.copyArea(0, 0, getSize().width, imgHeight, 0,
-vertical * av.getCharHeight());
gg.copyArea(0, 0, getSize().width, imgHeight, 0,
-vertical * av.getCharHeight());
- int ss = av.startSeq, es = av.endSeq, transY = 0;
+ int ss = av.getStartSeq(), es = av.getEndSeq(), transY = 0;
if (vertical > 0) // scroll down
{
ss = es - vertical;
if (vertical > 0) // scroll down
{
ss = es - vertical;
- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+ if (ss < av.getStartSeq()) // ie scrolling too fast, more than a page at a
+ // time
{
{
- ss = av.startSeq;
+ ss = av.getStartSeq();
}
else
{
}
else
{
@@
-122,9
+123,9
@@
public class IdCanvas extends Panel
else if (vertical < 0)
{
es = ss - vertical;
else if (vertical < 0)
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > av.getEndSeq())
{
{
- es = av.endSeq;
+ es = av.getEndSeq();
}
}
}
}
@@
-180,7
+181,7
@@
public class IdCanvas extends Panel
gg.setFont(italic);
gg.fillRect(0, 0, getSize().width, getSize().height);
gg.setFont(italic);
gg.fillRect(0, 0, getSize().width, getSize().height);
- drawIds(av.startSeq, av.endSeq);
+ drawIds(av.getStartSeq(), av.getEndSeq());
g.drawImage(image, 0, 0, this);
}
g.drawImage(image, 0, 0, this);
}
@@
-235,7
+236,7
@@
public class IdCanvas extends Panel
int rowSize = av.getEndRes() - av.getStartRes();
// Draw the rest of the panels
int rowSize = av.getEndRes() - av.getStartRes();
// Draw the rest of the panels
- for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
+ for (int ypos = hgap, row = av.getStartRes(); (ypos <= getSize().height)
&& (row < maxwidth); ypos += cHeight, row += rowSize)
{
for (int i = starty; i < alheight; i++)
&& (row < maxwidth); ypos += cHeight, row += rowSize)
{
for (int i = starty; i < alheight; i++)
diff --git
a/src/jalview/appletgui/OverviewPanel.java
b/src/jalview/appletgui/OverviewPanel.java
index
1b6df1d
..
0d3f058
100755
(executable)
--- a/
src/jalview/appletgui/OverviewPanel.java
+++ b/
src/jalview/appletgui/OverviewPanel.java
@@
-253,7
+253,6
@@
public class OverviewPanel extends Panel implements Runnable,
if ((int) (row * sampleRow) == lastrow)
{
sameRow++;
if ((int) (row * sampleRow) == lastrow)
{
sameRow++;
- continue;
}
else
{
}
else
{
@@
-261,10
+260,13
@@
public class OverviewPanel extends Panel implements Runnable,
hiddenRow = false;
if (hasHiddenRows)
{
hiddenRow = false;
if (hasHiddenRows)
{
+ // look for sequence in hidden rows
seq = av.getAlignment().getHiddenSequences()
.getHiddenSequence(lastrow);
if (seq == null)
{
seq = av.getAlignment().getHiddenSequences()
.getHiddenSequence(lastrow);
if (seq == null)
{
+ // didn't find in hidden rows, adjust the index and retrieve from
+ // full row set
int index = av.getAlignment().getHiddenSequences()
.findIndexWithoutHiddenSeqs(lastrow);
int index = av.getAlignment().getHiddenSequences()
.findIndexWithoutHiddenSeqs(lastrow);
@@
-272,6
+274,7
@@
public class OverviewPanel extends Panel implements Runnable,
}
else
{
}
else
{
+ // found in hidden rows, ergo this row is hidden
hiddenRow = true;
}
}
hiddenRow = true;
}
}
diff --git
a/src/jalview/appletgui/SeqCanvas.java
b/src/jalview/appletgui/SeqCanvas.java
index
5d6bb07
..
fd74c4a
100755
(executable)
--- a/
src/jalview/appletgui/SeqCanvas.java
+++ b/
src/jalview/appletgui/SeqCanvas.java
@@
-216,12
+216,12
@@
public class SeqCanvas extends Panel
// Its possible on certain browsers that the call to fastpaint
// is faster than it can paint, so this check here catches
// this possibility
// Its possible on certain browsers that the call to fastpaint
// is faster than it can paint, so this check here catches
// this possibility
- if (lastsr + horizontal != av.startRes)
+ if (lastsr + horizontal != av.getStartRes())
{
{
- horizontal = av.startRes - lastsr;
+ horizontal = av.getStartRes() - lastsr;
}
}
- lastsr = av.startRes;
+ lastsr = av.getStartRes();
fastPaint = true;
gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
fastPaint = true;
gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
@@
-229,7
+229,8
@@
public class SeqCanvas extends Panel
imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
-vertical * avcharHeight);
imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
-vertical * avcharHeight);
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+ int sr = av.getStartRes(), er = av.getEndRes(), ss = av.getStartSeq(), es = av
+ .getEndSeq(), transX = 0, transY = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
if (horizontal > 0) // scrollbar pulled right, image to the left
{
@@
-244,9
+245,10
@@
public class SeqCanvas extends Panel
else if (vertical > 0) // scroll down
{
ss = es - vertical;
else if (vertical > 0) // scroll down
{
ss = es - vertical;
- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+ if (ss < av.getStartSeq()) // ie scrolling too fast, more than a page at a
+ // time
{
{
- ss = av.startSeq;
+ ss = av.getStartSeq();
}
else
{
}
else
{
@@
-256,9
+258,9
@@
public class SeqCanvas extends Panel
else if (vertical < 0)
{
es = ss - vertical;
else if (vertical < 0)
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > av.getEndSeq())
{
{
- es = av.endSeq;
+ es = av.getEndSeq();
}
}
}
}
@@
-331,11
+333,12
@@
public class SeqCanvas extends Panel
if (av.getWrapAlignment())
{
if (av.getWrapAlignment())
{
- drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+ drawWrappedPanel(gg, imgWidth, imgHeight, av.getStartRes());
}
else
{
}
else
{
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ drawPanel(gg, av.getStartRes(), av.getEndRes(), av.getStartSeq(),
+ av.getEndSeq(), 0);
}
g.drawImage(img, 0, 0, this);
}
g.drawImage(img, 0, 0, this);
@@
-421,7
+424,7
@@
public class SeqCanvas extends Panel
av.setWrappedWidth(cWidth);
av.setWrappedWidth(cWidth);
- av.endRes = av.startRes + cWidth;
+ av.setEndRes(av.getStartRes() + cWidth);
int endx;
int ypos = hgap;
int endx;
int ypos = hgap;
diff --git
a/src/jalview/appletgui/SeqPanel.java
b/src/jalview/appletgui/SeqPanel.java
index
1352fe9
..
946fc2a
100644
(file)
--- a/
src/jalview/appletgui/SeqPanel.java
+++ b/
src/jalview/appletgui/SeqPanel.java
@@
-226,16
+226,16
@@
public class SeqPanel extends Panel implements MouseMotionListener,
}
else
{
}
else
{
- while (seqCanvas.cursorY < av.startSeq)
+ while (seqCanvas.cursorY < av.getStartSeq())
{
ap.scrollUp(true);
}
{
ap.scrollUp(true);
}
- while (seqCanvas.cursorY + 1 > av.endSeq)
+ while (seqCanvas.cursorY + 1 > av.getEndSeq())
{
ap.scrollUp(false);
}
while (seqCanvas.cursorX < av.getColumnSelection()
{
ap.scrollUp(false);
}
while (seqCanvas.cursorX < av.getColumnSelection()
- .adjustForHiddenColumns(av.startRes))
+ .adjustForHiddenColumns(av.getStartRes()))
{
if (!ap.scrollRight(false))
{
if (!ap.scrollRight(false))
@@
-244,7
+244,7
@@
public class SeqPanel extends Panel implements MouseMotionListener,
}
}
while (seqCanvas.cursorX > av.getColumnSelection()
}
}
while (seqCanvas.cursorX > av.getColumnSelection()
- .adjustForHiddenColumns(av.endRes))
+ .adjustForHiddenColumns(av.getEndRes()))
{
if (!ap.scrollRight(true))
{
{
if (!ap.scrollRight(true))
{
@@
-1643,8
+1643,8
@@
public class SeqPanel extends Panel implements MouseMotionListener,
oldSeq = -1;
}
oldSeq = -1;
}
- if (res > av.endRes || res < av.startRes || y < av.startSeq
- || y > av.endSeq)
+ if (res > av.getEndRes() || res < av.getStartRes()
+ || y < av.getStartSeq() || y > av.getEndSeq())
{
mouseExited(evt);
}
{
mouseExited(evt);
}
@@
-1890,8
+1890,8
@@
public class SeqPanel extends Panel implements MouseMotionListener,
public void scrollTo(int row, int column)
{
public void scrollTo(int row, int column)
{
- row = row < 0 ? ap.av.startSeq : row;
- column = column < 0 ? ap.av.startRes : column;
+ row = row < 0 ? ap.av.getStartSeq() : row;
+ column = column < 0 ? ap.av.getStartRes() : column;
ap.scrollTo(column, column, row, true, true);
}
ap.scrollTo(column, column, row, true, true);
}
@@
-1903,8
+1903,8
@@
public class SeqPanel extends Panel implements MouseMotionListener,
public void scrollToRow(int row)
{
public void scrollToRow(int row)
{
- row = row < 0 ? ap.av.startSeq : row;
- ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
+ row = row < 0 ? ap.av.getStartSeq() : row;
+ ap.scrollTo(ap.av.getStartRes(), ap.av.getStartRes(), row, true, true);
}
/**
}
/**
@@
-1915,8
+1915,8
@@
public class SeqPanel extends Panel implements MouseMotionListener,
public void scrollToColumn(int column)
{
public void scrollToColumn(int column)
{
- column = column < 0 ? ap.av.startRes : column;
- ap.scrollTo(column, column, ap.av.startSeq, true, true);
+ column = column < 0 ? ap.av.getStartRes() : column;
+ ap.scrollTo(column, column, ap.av.getStartSeq(), true, true);
}
/**
}
/**
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
b5fc817
..
75d3677
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-640,8
+640,10
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
- alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.getSeqPanel().seqCanvas.cursorX = viewport
+ .getStartRes();
+ alignPanel.getSeqPanel().seqCanvas.cursorY = viewport
+ .getStartSeq();
}
alignPanel.getSeqPanel().seqCanvas.repaint();
break;
}
alignPanel.getSeqPanel().seqCanvas.repaint();
break;
@@
-679,8
+681,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
else
{
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ alignPanel.setScrollValues(viewport.getStartRes(),
+ 2 * viewport.getStartSeq() - viewport.getEndSeq());
}
break;
case KeyEvent.VK_PAGE_DOWN:
}
break;
case KeyEvent.VK_PAGE_DOWN:
@@
-690,8
+692,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
else
{
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
+ alignPanel.setScrollValues(viewport.getStartRes(),
+ viewport.getEndSeq());
}
break;
}
}
break;
}
@@
-2612,7
+2614,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(viewport.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
@@
-2651,7
+2653,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(viewport.getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
3d0eb21
..
4c888a1
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-237,10
+237,10
@@
public class AlignViewport extends AlignmentViewport implements
void init()
{
void init()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
+ setStartRes(0);
+ setEndRes(alignment.getWidth() - 1);
+ setStartSeq(0);
+ setEndSeq(alignment.getHeight() - 1);
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
diff --git
a/src/jalview/gui/AlignmentPanel.java
b/src/jalview/gui/AlignmentPanel.java
index
d793e6a
..
552d166
100644
(file)
--- a/
src/jalview/gui/AlignmentPanel.java
+++ b/
src/jalview/gui/AlignmentPanel.java
@@
-467,7
+467,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
vscroll.setValue((res / cwidth));
if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
vscroll.setValue((res / cwidth));
- av.startRes = vscroll.getValue() * cwidth;
+ av.setStartRes(vscroll.getValue() * cwidth);
}
}
}
}
@@
-591,7
+591,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
fontChanged();
setAnnotationVisible(av.isShowAnnotation());
boolean wrap = av.getWrapAlignment();
fontChanged();
setAnnotationVisible(av.isShowAnnotation());
boolean wrap = av.getWrapAlignment();
- av.startSeq = 0;
+ av.setStartSeq(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
idwidthAdjuster.setVisible(!wrap);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
idwidthAdjuster.setVisible(!wrap);
@@
-810,8
+810,8
@@
public class AlignmentPanel extends GAlignmentPanel implements
overviewPanel.setBoxPosition();
}
overviewPanel.setBoxPosition();
}
- int scrollX = av.startRes - oldX;
- int scrollY = av.startSeq - oldY;
+ int scrollX = av.getStartRes() - oldX;
+ int scrollY = av.getStartSeq() - oldY;
if (av.getWrapAlignment() || !fastPaint)
{
if (av.getWrapAlignment() || !fastPaint)
{
@@
-821,13
+821,13
@@
public class AlignmentPanel extends GAlignmentPanel implements
{
// Make sure we're not trying to draw a panel
// larger than the visible window
{
// Make sure we're not trying to draw a panel
// larger than the visible window
- if (scrollX > av.endRes - av.startRes)
+ if (scrollX > av.getEndRes() - av.getStartRes())
{
{
- scrollX = av.endRes - av.startRes;
+ scrollX = av.getEndRes() - av.getStartRes();
}
}
- else if (scrollX < av.startRes - av.endRes)
+ else if (scrollX < av.getStartRes() - av.getEndRes())
{
{
- scrollX = av.startRes - av.endRes;
+ scrollX = av.getStartRes() - av.getEndRes();
}
if (scrollX != 0 || scrollY != 0)
}
if (scrollX != 0 || scrollY != 0)
diff --git
a/src/jalview/gui/AnnotationPanel.java
b/src/jalview/gui/AnnotationPanel.java
index
b1f0edb
..
c619dc1
100755
(executable)
--- a/
src/jalview/gui/AnnotationPanel.java
+++ b/
src/jalview/gui/AnnotationPanel.java
@@
-55,7
+55,6
@@
import java.util.List;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.Scrollable;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.Scrollable;
@@
-905,7
+904,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
return;
}
}
return;
}
}
- imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
+ imgWidth = (av.getEndRes() - av.getStartRes() + 1) * av.getCharWidth();
if (imgWidth < 1)
{
return;
if (imgWidth < 1)
{
return;
@@
-946,7
+945,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
imageFresh = true;
}
imageFresh = true;
}
- drawComponent(gg, av.startRes, av.endRes + 1);
+ drawComponent(gg, av.getStartRes(), av.getEndRes() + 1);
imageFresh = false;
g.drawImage(image, 0, 0, this);
}
imageFresh = false;
g.drawImage(image, 0, 0, this);
}
@@
-976,8
+975,8
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
gg.copyArea(0, 0, imgWidth, getHeight(),
-horizontal * av.getCharWidth(), 0);
long mtime = System.currentTimeMillis();
gg.copyArea(0, 0, imgWidth, getHeight(),
-horizontal * av.getCharWidth(), 0);
long mtime = System.currentTimeMillis();
- int sr = av.startRes;
- int er = av.endRes + 1;
+ int sr = av.getStartRes();
+ int er = av.getEndRes() + 1;
int transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
int transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
diff --git
a/src/jalview/gui/IdCanvas.java
b/src/jalview/gui/IdCanvas.java
index
37be8bc
..
c753cae
100755
(executable)
--- a/
src/jalview/gui/IdCanvas.java
+++ b/
src/jalview/gui/IdCanvas.java
@@
-161,17
+161,17
@@
public class IdCanvas extends JPanel
gg.copyArea(0, 0, getWidth(), imgHeight, 0,
-vertical * av.getCharHeight());
gg.copyArea(0, 0, getWidth(), imgHeight, 0,
-vertical * av.getCharHeight());
- int ss = av.startSeq;
- int es = av.endSeq;
+ int ss = av.getStartSeq();
+ int es = av.getEndSeq();
int transY = 0;
if (vertical > 0) // scroll down
{
ss = es - vertical;
int transY = 0;
if (vertical > 0) // scroll down
{
ss = es - vertical;
- if (ss < av.startSeq)
+ if (ss < av.getStartSeq())
{ // ie scrolling too fast, more than a page at a time
{ // ie scrolling too fast, more than a page at a time
- ss = av.startSeq;
+ ss = av.getStartSeq();
}
else
{
}
else
{
@@
-182,9
+182,9
@@
public class IdCanvas extends JPanel
{
es = ss - vertical;
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > av.getEndSeq())
{
{
- es = av.endSeq;
+ es = av.getEndSeq();
}
}
}
}
@@
-240,7
+240,7
@@
public class IdCanvas extends JPanel
gg.setColor(Color.white);
gg.fillRect(0, 0, getWidth(), imgHeight);
gg.setColor(Color.white);
gg.fillRect(0, 0, getWidth(), imgHeight);
- drawIds(av.getStartSeq(), av.endSeq);
+ drawIds(av.getStartSeq(), av.getEndSeq());
g.drawImage(image, 0, 0, this);
}
g.drawImage(image, 0, 0, this);
}
@@
-317,7
+317,7
@@
public class IdCanvas extends JPanel
int rowSize = av.getEndRes() - av.getStartRes();
// Draw the rest of the panels
int rowSize = av.getEndRes() - av.getStartRes();
// Draw the rest of the panels
- for (int ypos = hgap, row = av.startRes; (ypos <= getHeight())
+ for (int ypos = hgap, row = av.getStartRes(); (ypos <= getHeight())
&& (row < maxwidth); ypos += cHeight, row += rowSize)
{
for (int i = starty; i < alheight; i++)
&& (row < maxwidth); ypos += cHeight, row += rowSize)
{
for (int i = starty; i < alheight; i++)
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
3ac453f
..
55d29d5
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-1270,8
+1270,8
@@
public class Jalview2XML
view.setWidth(size.width);
view.setHeight(size.height);
view.setWidth(size.width);
view.setHeight(size.height);
- view.setStartRes(av.startRes);
- view.setStartSeq(av.startSeq);
+ view.setStartRes(av.getStartRes());
+ view.setStartSeq(av.getStartSeq());
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
diff --git
a/src/jalview/gui/SeqCanvas.java
b/src/jalview/gui/SeqCanvas.java
index
d015292
..
54d2be7
100755
(executable)
--- a/
src/jalview/gui/SeqCanvas.java
+++ b/
src/jalview/gui/SeqCanvas.java
@@
-279,10
+279,10
@@
public class SeqCanvas extends JComponent
gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
imgHeight, -horizontal * charWidth, -vertical * charHeight);
gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
imgHeight, -horizontal * charWidth, -vertical * charHeight);
- int sr = av.startRes;
- int er = av.endRes;
- int ss = av.startSeq;
- int es = av.endSeq;
+ int sr = av.getStartRes();
+ int er = av.getEndRes();
+ int ss = av.getStartSeq();
+ int es = av.getEndSeq();
int transX = 0;
int transY = 0;
int transX = 0;
int transY = 0;
@@
-300,9
+300,9
@@
public class SeqCanvas extends JComponent
{
ss = es - vertical;
{
ss = es - vertical;
- if (ss < av.startSeq)
+ if (ss < av.getStartSeq())
{ // ie scrolling too fast, more than a page at a time
{ // ie scrolling too fast, more than a page at a time
- ss = av.startSeq;
+ ss = av.getStartSeq();
}
else
{
}
else
{
@@
-313,9
+313,9
@@
public class SeqCanvas extends JComponent
{
es = ss - vertical;
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > av.getEndSeq())
{
{
- es = av.endSeq;
+ es = av.getEndSeq();
}
}
}
}
@@
-397,11
+397,12
@@
public class SeqCanvas extends JComponent
if (av.getWrapAlignment())
{
if (av.getWrapAlignment())
{
- drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+ drawWrappedPanel(gg, getWidth(), getHeight(), av.getStartRes());
}
else
{
}
else
{
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ drawPanel(gg, av.getStartRes(), av.getEndRes(), av.getStartSeq(),
+ av.getEndSeq(), 0);
}
g.drawImage(lcimg, 0, 0, this);
}
g.drawImage(lcimg, 0, 0, this);
@@
-503,7
+504,7
@@
public class SeqCanvas extends JComponent
av.setWrappedWidth(cWidth);
av.setWrappedWidth(cWidth);
- av.endRes = av.startRes + cWidth;
+ av.setEndRes(av.getStartRes() + cWidth);
int endx;
int ypos = hgap;
int endx;
int ypos = hgap;
diff --git
a/src/jalview/gui/SeqPanel.java
b/src/jalview/gui/SeqPanel.java
index
37b4852
..
16415cc
100644
(file)
--- a/
src/jalview/gui/SeqPanel.java
+++ b/
src/jalview/gui/SeqPanel.java
@@
-385,18
+385,18
@@
public class SeqPanel extends JPanel implements MouseListener,
}
else
{
}
else
{
- while (seqCanvas.cursorY < av.startSeq)
+ while (seqCanvas.cursorY < av.getStartSeq())
{
ap.scrollUp(true);
}
{
ap.scrollUp(true);
}
- while (seqCanvas.cursorY + 1 > av.endSeq)
+ while (seqCanvas.cursorY + 1 > av.getEndSeq())
{
ap.scrollUp(false);
}
if (!av.getWrapAlignment())
{
while (seqCanvas.cursorX < av.getColumnSelection()
{
ap.scrollUp(false);
}
if (!av.getWrapAlignment())
{
while (seqCanvas.cursorX < av.getColumnSelection()
- .adjustForHiddenColumns(av.startRes))
+ .adjustForHiddenColumns(av.getStartRes()))
{
if (!ap.scrollRight(false))
{
{
if (!ap.scrollRight(false))
{
@@
-404,7
+404,7
@@
public class SeqPanel extends JPanel implements MouseListener,
}
}
while (seqCanvas.cursorX > av.getColumnSelection()
}
}
while (seqCanvas.cursorX > av.getColumnSelection()
- .adjustForHiddenColumns(av.endRes))
+ .adjustForHiddenColumns(av.getEndRes()))
{
if (!ap.scrollRight(true))
{
{
if (!ap.scrollRight(true))
{
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
fb2b407
..
b728efc
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-1285,14
+1285,13
@@
public abstract class AlignmentViewport implements AlignViewportI,
*/
private boolean followHighlight = true;
*/
private boolean followHighlight = true;
- // TODO private with getters and setters?
- public int startRes;
+ private int startRes;
- public int endRes;
+ private int endRes;
- public int startSeq;
+ private int startSeq;
- public int endSeq;
+ private int endSeq;
/**
* Property change listener for changes in alignment
/**
* Property change listener for changes in alignment